Upcoming Events

For More Information:  deb@cs.cmu.edu

DNA read mapping is one of the fundamental problem in bioinformatics. The general goal is to map billions of short pieces of DNA (reads) to a high quality reference genome, while tolerating errors including genomic variations between individuals and the sequencer imprecision. The seed-and-extend strategy, a general mapping heuristic, efficiently maps erroneous DNA fragments to the reference by breaking the read into multiple non-overlapping segments, called "seeds", and assume at least one of the seed is error free. By using seed to index into the reference genome, seed-and-extend mappers drastically reduce the search space hence improves the run time. However, a fundamental trade-off of seed-and-extend mappers is the balance between seed lengths and seed count. Greater seed length further reduces the search space therefore improve the performance. However, greater seed space also renders fewer seeds hence make the mapping process more error prune. In this talk, I will present an on-going work, VEST (Versatile Error-resilient Seed Technique). VEST aims to adapt long seeds in order to make them error-resilient, hence achieves both high error tolerance as well as high mapping speed. Presented in Partial Fulfillment of the CSD Speaking Skills Requirement

Event Categories: Speaking Skills

For More Information:  deb@cs.cmu.edu

Cells need to be able to sustain themselves, divide, and adapt to new stimuli. Proteins arekey agents in regulating these processes. Cell behavior is regulated by signaling pathways and proteins called transcription factors which regulate what and how much of a protein should be manufactured. Anytime a new stimulus arises, it can activate multiple signaling pathways by interacting with proteins on the cell surface (if it is an external stimulus) or proteins within the cell (if it is a virus for example).Disruption in signaling pathways can lead to a myriad of diseases. Knowledge of which signaling pathways play a role in which condition, is thus key to comprehending how cells develop, react to environmental stimulus, and are able to carry out their normal functions. Another biological process that can play a role in such reaction is epigenetics -- modification of the DNA structure that do not involve changing the sequence itself. Epigenetics has been shown to regulate transcription, however, how epigenetic changes are regulated and the exact impact these changes have on transcriptional regulation are still open questions.In this thesis we present a suite of computational techniques that are focused on modeling the dynamic regulation of biological processes. These methods address the various aspects of the problem mentioned above focusing on the reconstruction of dynamic signaling and regulatory networks. In many cases, the amount of biological data available for a specific condition can be very small compared to the number of variables. We present an algorithm which uses multi-task learning to learn signaling networks from many related conditions. There are also very few tools that attempt to take temporal dynamics into account when inferring signaling networks. The thesis presents a new algorithm that utilizes and extends Integer Programming methods for inferring such dynamic regulation. Finally, we present a new strategy to integrate epigenetic data with other temporal datasets using deep neural networks. We use this new method to reconstruct dynamic disease progression networks in Idiopathic Pulmonary Fibrosis (IPF).Thesis Committee:Ziv Bar-Joseph (Chair)Eric XingJaime CarbonellNaftali Kaminski (Yale University)

Event Categories: Thesis Oral

For More Information:  dhyde@cs.cmu.edu

4:15 social time, 4:30 meeting start (date moved back a week due to R&P)

Event Categories: Faculty Meeting

|  http://www.cmu.edu/student-affairs/family-weekend/ http://www.cmu.edu/student-affairs/family-weekend/

Family Weekend is an informative, engaging and important yearly tradition. Over the course of the Weekend, Carnegie Mellon welcomes parents and families to visit campus in order to interact with the organizations, people and places that have become important to your student. Each year,  a variety of recreation, social and cultural events, including varsity athletics, topical and interesting programs by faculty and staff, academic programming presentations, student performances and exhibits, welcome families to participate.

Event Categories: Academic Calendar Highlight

Business Office Open.  No classes.Classes resume Monday, October 23

Event Categories: Academic Calendar Highlight

For More Information:  dhyde@cs.cmu.edu

3:30 social time, 3:45 meeting start

Event Categories: Faculty Meeting

|  http://www.alumni.cmu.edu/s/1410/alumni/index-social.aspx?sid=1410&gid=1&pgid=35...|  http://www.alumni.cmu.edu/s/1410/alumni/index-social.aspx?sid=1410&gid=1&pgid=35...|  For More Information:  alumni-house@andrew.cmu.edu

Homecoming Tailgate!  Tartans take on the Case Western Reserve Spartans in the Academic Bowl at 2 p.m.Some highlights include:Carnegie Mellon University’s 50th anniversary celebrationTailgate LunchSenior day activitiesVeteran’s Day celebration

Event Categories: Academic Calendar Highlight

For More Information:  dhyde@cs.cmu.edu

4:15 social time, 4:30 meeting start

Event Categories: Faculty Meeting

For More Information:  deb@cs.cmu.edu

AI / Theory - years 1-3

Event Categories: Faculty Meeting

For More Information:  deb@cs.cmu.edu
Event Categories: Faculty Meeting

For More Information:  deb@cs.cmu.edu

General Meeting - Years 4-n

Event Categories: Faculty Meeting